Industrial Applications of Soil Microbes

For human beings, the diversity of microorganisms is still an undiscovered aspect. For the well-being of society, the huge microbial population performs many vital activities. Microorganisms play an important role in sustainable agriculture, environmental protection, and human and animal health. Microorganisms have a major contribution to agricultural issues like crop productivity, plant health protection, soil health maintenance, and environmental issues like bioremediation of soil and water from many pollutants. In addition to these activities, microorganisms also produce many products, either directly or through industrial processes, which are essential for human survival. In this chapter, we deal with various industrial products that are produced by microorganisms through different reactions, like antibiotics, enzymes, natural food preservatives, vitamins, fermentation products, amino acids, and agricultural products.

There are many bacteria in the soil, but they have less biomass because of their small size. Soil-inhabitant bacteria are an essential source of nutrients for plants. Some studies highlighted their industrial importance, like in the pharmaceutical industry, perfume manufacturing, and agriculture product scale-up production, including biofertilizers. Most of the studies have been carried out on Actinobacteria and Nitrobacter because of their potential to produce biofertilizers and chemical constituents on a large scale. This chapter discussed their taxonomic and morphological characteristics and gathered details about their practical applications from limited studies carried out in this field.

Indiscriminate use of agrochemicals to ramp up production capabilities has caused a considerable decline in soil health status. The growing awareness of their ill effects on the environment and human health has called for a reversion to old organic agricultural practices blended with modern-day science and technology. Soil microorganisms with an identified ability to support plant growth are now being deployed in the form of biofertilizers and microbial biocontrol agents. Other than augmenting nutrition supply, these bio-inoculums can synthesize phytohormones and can also enhance the micronutrient and organic content of the soil. They can further induce resistance in plants against phytopathogens and compete against them by secreting secondary metabolites to keep the pathogenic population in check. Soil microorganisms, due to their omnipresence and survivability on varied substrates and in different environmental conditions, also find their use in other applications such as in the mining and energy industries. Unlike conventional metallurgical practices that deplete high-grade mineral ore reserves and cause wide-scale destruction of habitats, bioleaching provides a safe and cheap prospect for the recovery of metals. Other than the extraction of precious metals from low-grade ores, they also find their use in metal recovery from e-waste and can even remove heavy metals from soil. Moreover, the rapidly developing mining and the agrochemical industry count upon fossil fuels to meet their energy needs. In the final section of this chapter, we discuss a yet fascinating aspect of how non-conventional sources of energy are produced by the action of soil microorganisms to minimize strains on fossil fuel reserves. These biofuels, produced by the transformation of organic biomass, have an edge over fossil fuels as they emit low levels of particulate matter, sulphur dioxide, and carbon monoxide.

Commodity chemicals are the intermediates that are generally involved in the synthesis of other high-end products. The increasing demand for various industrial products has upscaled the requirement for commodity chemicals. Originally, the industrial sector was dependent upon conventional and toxic chemicals to sustain its processes. However, the advent of biotechnology led to the development of numerous microbial processes producing enzymes, extremozymes, organic acids, organic solvents, etc., Moreover, the soil environment has diverse forms of microbial communities performing assorted functions. As a result, a thorough understanding of the soil microbiota involved in providing regulatory ecosystem services can aid in the development of exceptional microbial strains capable of meeting the high demand for these commodity chemicals. In addition, the exploitation of these excellent manipulative microbial systems can improve and customize the synthesis of commodity chemicals and thereby reduce the reliance on synthetic and petroleumbased products. This chapter will inform the readers about the applications of soil microbes in industry and their involvement in enzymes, extremozymes, organic acids, and biopigments production. 

Microbial biopesticides involve various microorganisms such as bacteria, fungi, viruses, nematode-associated bacteria, protozoans, and endophytes working against invertebrate pathogens in agro-ecosystems. Such novel biopesticidal products, after extensive research work, have been explored in the global market to combat synthetic pesticide application adverse problems. Recent academic and industrial efforts are involved in the discovery of toxins and virulence factors from microbial species for the synthesis of commercial formulations. The current review is the expansion of the application of various bacteria, fungi, viruses, nematodes, protozoans, and endophytes for biopesticide formulations and their role in pest management.

Soil is one of the principal ingredients of the universe, which supports all forms of life directly or indirectly. Soil consists of a mixture of various organic and inorganic matter, fluids, gases, and micro and macro-living systems and acts as a major living medium for a wide group of living organisms. One of the important soil inhabitants are microorganisms. Soil microorganisms can be categorized as bacteria, fungi, actinomycetes, protozoa, algae, and viruses. These microbes have varied features and functions. Most importantly, these microorganisms do not exist in isolation but interact with each other and contribute significantly to overall soil fertility. Many of these organisms have the capacity to produce antimicrobial substances as a defense mechanism to compete with other organisms for their survival and existence. Most of these antimicrobial substances, which are released as metabolites produced during trophophase as well as in idiophase, are medically significant in the treatment of many life-threatening infections in plants and animals. This chapter describes various soil microflora and their roles in the production of different kinds of antimicrobials. The primary goal is to familiarise readers with the various microflora found in soil and their ability to produce anti-microbial components.

 As the world’s population is increasing rapidly, there is an urgent need to increase crop production. To achieve this goal, an eco-friendly alternative to chemical fertilizers and pesticides is required. Several types of microbes have been identified inhabiting the plant rhizosphere, such as nitrogen-fixing bacteria, plant growthpromoting rhizobacteria, fungi, proteobacteria, mycoparasitic and mycorrhizal fungi. These microorganisms not only influence the growth and development of plants but also suppress pathogenic microbes near plant roots through several different mechanisms. Non-symbiotic microbes play a crucial role in the biogeochemical cycling of organic and inorganic phosphorus (P) near the root zone via solubilization and mineralization of P from total soil phosphorus. Additionally, some non-pathogenic microbes have also been reported to induce systemic resistance in plants, which is phenotypically similar to pathogen-induced systemic acquired resistance (SAR). The present review summarizes the latest knowledge on the role of non-pathogenic strains of microbiomes residing in the rhizosphere and their commercial applications. 

Bioremediation of environmental pollutants and contaminants in soil is an emerging technology, which will gain relevance and importance in the near future. Microbiological bioremediation is not only cost-effective but also environmentally sustainable, as it does not cause undesirable effects like toxic byproducts or residues, requires heavy infrastructure, has on-site application, and is the least hazardous to human health. With new biotechnological tools, the microbes can be designed to have desirable effects for the bioremediation of more toxic wastes. However, the free release of genetically modified microbes for this purpose is still under risk assessment. This is an effective method to use indigenous microflora and harness their biodegradation properties to remove unwanted contaminants from soil, water bodies, underground water aquifers, ocean spills, etc. Currently, they are mostly used for cleaning oil spills and removing petroleum products and heavy metals from soil. Both in situ and ex situ methods are employed, where microbes can be used in varied ways. Much work is going on to explore and enhance the properties of microbes, especially bacteria, to be used as agents for contaminant removal from our environment. Global bioremediation is an emerging market that is slowly growing and will become a multibillion-dollar market worldwide in days to come. The current review tries to view the subject with microbes in perspective; their role in bioremediation; mode of action; technologies used; and their use for sustainable cleanup of the environment. 

Agricultural production is majorly hampered by the negative impact of both biotic and abiotic stress in most developing countries. Among abiotic stresses, soil salinity is a major problem, affecting crop production and responsible for limiting the growth and productivity of plants in different areas of the world due to increasing use of poor quality of water, flooding, over-irrigation, seepage, silting, and a rising water table. In agriculture, salt-tolerant rhizospheric/endophytic microorganisms play an important role in helping alleviate abiotic stresses in plants. Under plant-microbe interactions, plant root-associated microbes, including endophytes, closely interact and cooperate with plants, and mediate important physiological and metabolic processes, thereby enhancing the plant’s tolerance to salinity stress. Several mechanisms have been developed for microbial alleviation of salinity stress in plants, including the production of phytohormones, improving plant nutrient status, production of ACC deaminase, salt exclusion, and enhancing resistance to drought in plant cells. A wide range of micro-organisms are available that have diverse mechanisms for salt stress alleviation in plants. Future research needs to be directed towards field evaluation for the validation of the potential microbes. 

The degradation of wood is a highly complex process involving the activities of several different microbes. It has been explored through research that microorganisms have developed various strategies (enzymatic and nonenzymatic) to utilize wood. In the present article, we are presenting the enzymes that originated from fungi and bacteria and their reactions to decomposing wood. Analysis of enzymes involved in wood degradation will not only be helpful in the study of the wood degradation process but also provide information about various ecological niches of the microorganisms. Genomic and secretome data have revealed the importance of the enzymes secreted by microorganisms such as fungi and bacteria in wood degradation in ecological niches. 

The agricultural economy has been suffering from various pathogenic diseases of crops, fruits, grains, and vegetables for a long time. Controlling these diseases is pivotal to the growth of agricultural production and the availability of harvests. Compared with relatively harmful chemical agents, biocontrol agents are now being used as safer and less toxic alternatives to control crop losses. Yeasts survive in all environmental conditions and have been described as potent antagonists to various plant pathogens. Due to their antagonistic activity towards pathogens, relatively simple cultivation requirements, and very limited biosafety concerns, many of these unicellular fungi are being considered for biocontrol applications. In this chapter, we have discussed the pros and cons of yeasts as biocontrol agents, various yeast species, and their modes of antagonistic action. To survive in the environment, yeasts need to tolerate various biotic and abiotic stresses. Those stresses have been discussed here, and how different yeast strains overcome these harsh conditions and carry out antagonistic activities have also been highlighted. Yeast biocontrol activities to date represent a largely unexplored field of research and plenty of opportunities remain for the development of commercial, yeast-based applications for plant protection. 

Macrophomina phaseolina (Tassi) Goid. is a destructive fungal soil microbe, a cause of charcoal rot disease and causes heavy losses in agricultural production. It is non-specific and appears in moderate to severe form every year worldwide. Due to the seriousness and economic importance of the pathogen as well as disease, it requires multiple approaches like epidemiological study, induction of systemic resistance through non-conventional chemicals, host-pathogen resistance and chemical as well as phytoextract application for its management. Epidemiological studies reveal that the onset of charcoal rot varied in different varieties during different dates of sowing. Timely sowing of crops is an important tool for reducing disease incidence. The intensity of disease in a timely sown crop is less, with higher production and productivity. The non-conventional chemicals like salicylic acid, acetylsalicylic acid, indole acetic acid, indole butyric acid, riboflavin, and thiamine induce systemic acquired resistance (SAR) and effectively inhibit mycelial growth of the pathogen. These non-conventional chemicals showed a reduction of charcoal rot disease under field conditions. It also enhances the yield-attributing traits and yield. It induces total phenol content, peroxidase, polyphenol oxidase, phenylalanine ammonia lyase, and catalase activity by the treatment of these chemicals. These activities showed a differential reaction after inoculation of the pathogen on different varieties. However, resistant varieties showed higher induction of biochemical activities than susceptible ones. Different phytoextracts showed inhibition of mycelial growth and a reduction of disease incidence in different crops. Seed treatment with fungicides is an effective method for controlling the pathogen and ultimately enhances the production of the crop. Genotype evaluation for host resistance is an effective, economical, and continuous way of managing the pathogen and disease. 

In the present day perspective, with the increasing cost of chemical pesticides along with increasing incidences of pesticide toxicity, the application of microbial pesticides holds good promise for crop protection around the world. Beauveria bassiana is a common soil fungus, having a broad host range and therefore is used for biological control of soil-dwelling insect pests. As this fungus is epizootic, it is being used worldwide as a biopesticide to control several pests, such as termites, whiteflies, and malaria-transmitting mosquitoes. The use of this fungus in different crop protection systems significantly controls the Colorado potato beetle, codling moth, and several genera of termites and bollworms. As insecticides, the spores are sprayed on affected crops as an emulsified suspension or wettable powder. Generally, B. bassiana is considered a nonselective pesticide because it parasitizes a very high range of arthropod hosts. This entomopathogenic fungus is also applied against the European and Indian corn borer, pine caterpillar, and green leafhoppers. The ability of B. bassiana to antagonize, parasitize, and kill insects endorses it as an efficient biocontrol agent. Although B. bassiana has a good share in the total biopesticide market, there is still ample scope for further development of this superior strain through advertisement among the farming community. 

Many fungi are directly or indirectly toxic to humans and animals. Ergot, a fruiting body of the Claviceps purpurea fungus, contaminates grain after harvest and is toxic to humans and animals who consume contaminated grains. The lysergic acid diethylamide (LSD) that was widely used as a hallucinogen is best known as the ergot alkaloids. The main symptoms of the disease caused by consuming ergot-contaminated grain flour in humans and animals are blistering and reddening of the skin with a burning sensation. Ergot alkaloids such as agroclavine, ergovaline, ergotamine, ergonovine, lysergic acid, dopamine, etc., are the natural alkaloids produced by Claviceps spp. in many cereal crops (mainly wheat, barley, rye, bajra, jowar, and dallisgrass), but rye (triticale) is the most common host of this fungus. Contaminated grain may cause very harmful diseases to internal organs, the circulatory and nervous systems of animals and humans, and even they may die. Ergot alkaloids are very important in the pharmaceutical industry. Therefore, this soil-borne fungus, which can be used in the manufacturing of different types of medicines for human and animal welfare, is very important.

Microbial inhabitants of soil are in an active state and change in response to modifications in environmental conditions, amendments, management, etc. Although various methods have been developed to study the biological properties of a disturbed soil sample or with their precincts, adoption of a method should be done keeping in mind the objective, limitations and assumptions of the method. Reproducibility of results is important to have broad applicability and comparisons, which in turn will depend upon effectiveness. Soil is a diverse medium having varying physicochemical properties, and hence, there should be modifications while standardizing the method. It will help in getting reproductive results. Sampling, processing, and storage of samples are equally important to have a true picture of the soil and need appropriate care. The numbers and kinds of fungi on the root surface, i.e., rhizoplane of the leguminous crop plant and in the rhizosphere (near the roots), have been compared with the number and kinds in root-free soil. The crops showed a typical rhizosphere effect, and there were more microorganisms in the rhizosphere than in root-free soil. A total of 34 different species of fungi were identified. The majority belong to the Aspergillus genus. Roots and the rhizosphere of moth bean (Vigna aconitifolia) yielded a higher proportion of fungi than did root-free soil

The genus Trichoderma (fungi) is a very large group of microorganisms that play a significant role in the environment. This is omnipresent in the climate, particularly in soils. Trichoderma species could be easily isolated from the soil by all traditional methods available because of their rapid growth and abundant conidiation. These are used both as biofungicides for biological plant protection as well as for bioremediation. In addition, the genus Trichoderma includes edible and medicinal mushrooms but also human pathogens. Members of the Trichoderma genus are often used primarily in the processing of enzymes, antibiotics, and other metabolites, but also for biofuel in various branches of industry. Several researchers have confirmed, based on phylogenetic analysis, that Trichoderma and Hypocrea form a single holomorphic genus. In which two can be differentiated by large clades. Several Trichoderma spp. positively affect plants by stimulating plant growth and protecting plants from fungal and bacterial pathogens. Trichoderma has entered the genomic period at present, and sections of the genome sequences are open to the public. For this purpose, Trichoderma can be used to an even greater degree than before for human needs. Trichoderma species possess diverse biotechnological applications, such as acting as biofungicides to control various plant diseases and as biofertilizers to promote plant production. Trichoderma secretes various volatile compounds, including alcohols, aldehydes, ketones, ethylene, hydrogen cyanide, and monoterpenes, as well as non-volatile compounds known to exhibit antibiotic activity, including peptaibols, and diketopiperazine-like gliotoxins and gliovirins. Nonetheless, further studies are required to make the application of these fungi more effective and safe.